I just pretend the question contains questions:
- What is the warning concerning
titlesec about?
- Why are my headers looking horrible?
1) The classicthesis template uses scrreprt with the option headinclude and footinclude, which are passed over to package typearea.
Package classicthesis defines the size of the typeblock, ensuring that package typearea is loaded, but not taking into account the options passed to it. So you have to always add the options globally. Or use package geometry to change the margins, which makes using the package classicthesis pointless, as it only defines the style.
2) Opposed to it, the author of classicthesis decided to tweak the appearance of sectional headings using package titlesec, which in the meantime issues a quite prominent warning by KOMA-script, because it breaks some KOMA functionality.
You can (probably) silence the warnings, but that does not fix the fact, that classicthesis is in wide parts incompatible with KOMA-script.
A little example:
\documentclass[
% headinclude,footinclude,% option for tyearea
headings=optiontoheadandtoc
]{scrreprt}
\usepackage{blindtext}
\usepackage{classicthesis}% destroys head/toc mechanism using titlesec
\begin{document}
\pagestyle{headings}
\tableofcontents
\chapter[head={Walter Wombat}, tocentry={Gerry
Giraffe}]{Lyndon Lizard}% kicked by titlesec
\blindtext[10]
\end{document}
titlesecis not compatible with KOMA too. I think, there are a lot of questions that deal with this issue and you've been told so already, as far as I can remember – Feb 28 '16 at 17:12classicthesisassumes the KOMA-optionheadincludeandfootinclude, else the header will be on the edge of the page. – Johannes_B Feb 28 '16 at 17:16classicthesisreally just defines a bit of the optical appearance. All functionality, chapters, sections, referencing and citing, list generation etc. is basic LaTeX functiionality and available without any template. – Johannes_B Feb 28 '16 at 17:19